| Title: | Save and Load Spatial 'Omics Data to/from File |
|---|---|
| Description: | Save SpatialExperiment objects and their images into file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties. |
| Authors: | Aaron Lun [aut, cre] |
| Maintainer: | Aaron Lun <[email protected]> |
| License: | MIT + file LICENSE |
| Version: | 1.7.1 |
| Built: | 2024-11-10 03:26:00 UTC |
| Source: | https://github.com/bioc/alabaster.spatial |
Load an image as a SpatialImage or subclass thereof.
loadSpatialImage(img.info, project)loadSpatialImage(img.info, project)
img.info |
Named list containing the metadata for this assay. |
project |
Object specifying the project of interest. |
A SpatialImage containing the image data (or a reference to it).
Aaron Lun
example(read10xVisium, echo=FALSE) img <- imgData(spe)$data[[1]] tmp <- tempfile() dir.create(tmp) meta <- stageObject(img, tmp, "whee") out <- loadSpatialImage(meta, tmp)example(read10xVisium, echo=FALSE) img <- imgData(spe)$data[[1]] tmp <- tempfile() dir.create(tmp) meta <- stageObject(img, tmp, "whee") out <- loadSpatialImage(meta, tmp)
Read a SpatialExperiment object from its on-disk representation.
readSpatialExperiment(path, metadata, ...)readSpatialExperiment(path, metadata, ...)
path |
String containing a path to a directory, itself created using the |
metadata |
Named list of metadata for this object, see |
... |
Further arguments passed to |
A SpatialExperiment object.
Aaron Lun
"saveObject,SpatialExperiment-method", to save a SpatialExperiment to disk.
library(SpatialExperiment) example(read10xVisium, echo=FALSE) tmp <- tempfile() saveObject(spe, tmp) readObject(tmp)library(SpatialExperiment) example(read10xVisium, echo=FALSE) tmp <- tempfile() saveObject(spe, tmp) readObject(tmp)
Save a SpatialExperiment object to its on-disk representation.
## S4 method for signature 'SpatialExperiment' saveObject(x, path, ...)## S4 method for signature 'SpatialExperiment' saveObject(x, path, ...)
x |
A SpatialExperiment object. |
path |
String containing the path to a directory in which to save |
... |
Additional named arguments to pass to specific methods. |
Currently, only PNG and TIFF image formats are supported in the imgData.
All other images will be re-saved as PNG.
x is saved to path and NULL is invisibly returned.
Aaron Lun
readSpatialExperiment, to read the SpatialExperiment back into the R session.
library(SpatialExperiment) example(read10xVisium, echo=FALSE) tmp <- tempfile() saveObject(spe, tmp) list.files(tmp, recursive=TRUE)library(SpatialExperiment) example(read10xVisium, echo=FALSE) tmp <- tempfile() saveObject(spe, tmp) list.files(tmp, recursive=TRUE)
These methods are deprecated and are only documented here for back-compatibility purposes.
## S4 method for signature 'VirtualSpatialImage' stageObject(x, dir, path, child = FALSE, ...) ## S4 method for signature 'StoredSpatialImage' stageObject(x, dir, path, child = FALSE, ...) ## S4 method for signature 'RemoteSpatialImage' stageObject(x, dir, path, child = FALSE, ...)## S4 method for signature 'VirtualSpatialImage' stageObject(x, dir, path, child = FALSE, ...) ## S4 method for signature 'StoredSpatialImage' stageObject(x, dir, path, child = FALSE, ...) ## S4 method for signature 'RemoteSpatialImage' stageObject(x, dir, path, child = FALSE, ...)
x |
A SpatialImage object. |
dir |
String containing a path to a directory. |
path |
String containing a relative path inside a directory. |
child |
Logical scalar indicating whether |
... |
Further arguments, ignored. |
Each of the different methods will take advantage of any existing files to avoid an actual save.
For example, the RemoteSpatialImage method will download the file directly to path,
while the StoredSpatialImage method will create a link or copy the file.
The SpatialImage method will fall back to saving the raster directly as a PNG.
An image file is created at file.path(dir, path), possibly after appending an appropriate file extension.
The return value should be a named list containing at least:
$schema, a string specifying the schema to use to validate the metadata.
This may have a package attribute to specify the package where the schema lives (in its inst/schemas directory).
path, a string containing the path to the file containing the assay contents.
This should start with the input path but can be followed by any necessary file extensions.
child, whether this is a child resource of a larger object.
Other fields can be provided and will be included in the metadata, provided that they are recognized by the specified schema.
Aaron Lun
example(read10xVisium, echo=FALSE) (img <- imgData(spe)$data[[1]]) # Doing a local run: tmp <- tempfile() dir.create(tmp) stageObject(img, tmp, "whee") # Forcing a re-save: Y <- as(img, "LoadedSpatialImage") stageObject(Y, tmp, "foo")example(read10xVisium, echo=FALSE) (img <- imgData(spe)$data[[1]]) # Doing a local run: tmp <- tempfile() dir.create(tmp) stageObject(img, tmp, "whee") # Forcing a re-save: Y <- as(img, "LoadedSpatialImage") stageObject(Y, tmp, "foo")